[Debian-med-packaging] Bug#722650: grinder, libbio-perl-perl: error when trying to install together

[Andreas Tille]

Hi,

the problem is fixed in Git - no reason to spend time in further tagging
+ checking versions etc.  Will upload until noon.

Thanks for all your work in these tests!!

  Andreas.

On Fri, Sep 13, 2013 at 04:15:10AM +0200, Andreas Beckmann wrote:
> Package: grinder,libbio-perl-perl
> Version: 1.6.920-1
> Severity: serious
> User: treinen at debian.org
> Usertags: edos-file-overwrite
> 
> Architecture: amd64
> Distribution: sid
> 
> Hi,
> 
> automatic installation tests of packages that share a file and at the
> same time do not conflict by their package dependency relationships has
> detected the following problem:
> 
>   Selecting previously unselected package grinder.
>   Unpacking grinder (from .../grinder_0.5.3-2_all.deb) ...
>   dpkg: error processing /var/cache/apt/archives/grinder_0.5.3-2_all.deb (--unpack):
>    trying to overwrite '/usr/share/man/man3/Bio::SeqFeature::Amplicon.3pm.gz', which is also in package libbio-perl-perl 1.6.920-1
>   dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
> 
> This is a serious bug as it makes installation fail, and violates
> sections 7.6.1 and 10.1 of the policy. An optimal solution would
> consist in only one of the packages installing that file, and renaming
> or removing the file in the other package. Depending on the
> circumstances you might also consider Replace relations or file
> diversions. If the conflicting situation cannot be resolved then, as a
> last resort, the two packages have to declare a mutual
> Conflict. Please take into account that Replaces, Conflicts and
> diversions should only be used when packages provide different
> implementations for the same functionality.
> 
> Here is a list of files that are known to be shared by both packages
> (according to the Contents file for sid/amd64, which may be
> slightly out of sync):
> 
> usr/share/man/man3/Bio::DB::IndexedBase.3pm.gz
> usr/share/man/man3/Bio::Seq::SimulatedRead.3pm.gz
> usr/share/man/man3/Bio::SeqFeature::Amplicon.3pm.gz
> usr/share/man/man3/Bio::SeqFeature::SubSeq.3pm.gz
> usr/share/man/man3/Bio::Tools::AmpliconSearch.3pm.gz
> usr/share/perl5/Bio/DB/IndexedBase.pm
> usr/share/perl5/Bio/Seq/SimulatedRead.pm
> usr/share/perl5/Bio/SeqFeature/Amplicon.pm
> usr/share/perl5/Bio/SeqFeature/SubSeq.pm
> usr/share/perl5/Bio/Tools/AmpliconSearch.pm  
> 
> This bug is assigned to both packages. If you, the maintainers of
> the two packages in question, have agreed on which of the packages will
> resolve the problem please reassign the bug to that package. You may
> also register in the BTS that the other package is affected by the bug.
> 
> Cheers,
> 
> Andreas
> 
> PS: for more information about the detection of file overwrite errors
> of this kind see http://edos.debian.net/file-overwrites/.


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